DNA sequencing is undergoing rapid development in the past several years. Highly efficient DNA sequencing systems are commercially available. A critical step in the use of these new DNA sequencing technologies is the preparation of nucleic acid libraries for sequencing. It is of interest to provide new and improved methods of generating libraries. Many nucleic acid library techniques involve a nucleic acid amplification step or steps. Such amplification steps can introduce representational biases into the libraries. Such application biases can make it difficult to obtain an accurate analysis of the nucleic acid samples under study. Accordingly, applicants provide herein new and improved methods and compositions for generating nucleic acid libraries for use in numerous DNA sequencing systems.